Topic outline

  • General


    Whole genome sequencing work-shop

    1-2 October 2015, Lausanne


    This 2-days work-shop, organized by the Doctoral Program in Molecular Plant Sciences, will be held in Lausanne on the 1st & 2nd of October 2015 . It is addressed to molecular plant biologists with few or no UNIX experience who are interested to learn ways to use NGS in order to identify mutations in model organisms after mutagenesis.

    On the second day of this workshop students will have the possibility to learn and execute each step of SNP detection analysis from the sequenced raw-reads to the final detection of the causal mutation.


    Debora Gasperini, University of Lausanne
    Laurent Falquet, Department of Biology, University of Fribourg
    Hannes Svardal, Gregor Mendel Institute, Austria
    Emanuel Schmid, Vital-IT, SIB Swiss Institute of Bioinformatics


    Application is open. Deadline for application is set to 28 September.


    Please bring your own laptop and verify that it fullfils the following requirements:

    • 30 GB of free space
    • 4GB RAM
    • working WIFI (guest accounts will be provided)

    Please follow prior the workshop the online learning module UNIX Fundamentals ( 


    Both, the lectures and the hands-on part will take place in the room 340.1 in the Amphipole (see map).


    For further information about the course and how to apply, please visit  the Molecular Plant Sciences page.

  • Programme

    Day 1

    8.30 - 8.45 Welcoming

    8.45 - 9.45 Session 1 : Debora Gasperini - Biological background, EMS mutagenesis, designing screens, importance of ploidy,..

    9.45 - 10.00 Coffee break

    10.00 - 11.00 Session 1 (second part)

    11.00 - 12.00 Session 2 : Laurent Falquet - Genome sequencing and assembly

    12.00 - 13.00 lunch break

    13.00 - 14.00 Session 2 (second part)

    14.00 - 15.00 Session 3 (first part)

    15.00 - 15.15 coffee break

    15.15 - 16.15 Session 3 : Hannes Svardal - SNP detection and analysis

    16.15 - 17.00  preparations for the hands-on part

    Day 2

    9.00 - 16.00: Practicals

    • raw sequencing read analysis
    • read mapping onto the ATH genome
    • haplotype calling & SNP detection
    • SNP evaluation

    Coffee break: 09h45, 14h40
    Lunch break: 12h00

  • Material